Cursor coordinates off during resolution change

So far I have full-screen working perfectly. It changes display modes, and shows the graphics without problem. However, whenever I change display modes within the game, the cursor coordinates are completely messed up. It seems like the scale is correct (except a little off when going between widescreen and standard ratios), it's just offset by a certain number of pixels depending on the new mode. Is there any way of resetting the rectangle used for cursor events? (without using a window, of course)

I achieve fullscreen by using CGDisplayCapture and CGDisplayBestModeForParameters/CGDisplaySwitchToMode. When I change resolutions, I use CGDisplayBestModeForParameters/CGDisplaySwitchToMode, but I also tried releasing and re-capturing the display, and also changing back to the original desktop resolution before releasing the display to no avail. Any help would be appreciated.

Edit: to clarify, the first resolution change when launching the game doesn't effect the cursor coordinates, it's only when changing the resolution from my options menu after launching the game.